Your description suggests you may be using 'Track Changes', which means both the original reference and the updated reference will be present until the changes are accepted/rejected.

Otherwise, without actually seeing the problem document, it can be difficult for anyone to diagnose the issue. Can you attach a document to a post with some representative data (delete anything sensitive)? You do this via the paperclip symbol on the 'Go Advanced' tab at the bottom of this screen.

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Cheers,
Paul Edstein
[Fmr MS MVP - Word]